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- PDB-4xq3: Crystal structure of Sso-SmAP2 -

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Basic information

Entry
Database: PDB / ID: 4xq3
TitleCrystal structure of Sso-SmAP2
ComponentsLike-Sm ribonucleoprotein core
KeywordsRNA BINDING PROTEIN / Archael proteins
Function / homology
Function and homology information


Sm-like protein family complex / mRNA splicing, via spliceosome / ribonucleoprotein complex / RNA binding
Similarity search - Function
SH3 type barrels. - #100 / Sm-like protein Lsm6/SmF / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. / LSM domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Like-Sm ribonucleoprotein core
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsBezerra, G.A. / Martens, B. / Kreuter, M.J. / Grishkovskaya, I. / Manica, M. / Arkhipova, V. / Blasi, U. / Djinovic-Carugo, K.
CitationJournal: Life / Year: 2015
Title: The Heptameric SmAP1 and SmAP2 Proteins of the Crenarchaeon Sulfolobus Solfataricus Bind to Common and Distinct RNA Targets.
Authors: Martens, B. / Bezerra, G.A. / Kreuter, M.J. / Grishkovskaya, I. / Manica, A. / Arkhipova, V. / Djinovic-Carugo, K. / Blasi, U.
History
DepositionJan 18, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Like-Sm ribonucleoprotein core
B: Like-Sm ribonucleoprotein core
C: Like-Sm ribonucleoprotein core
D: Like-Sm ribonucleoprotein core
E: Like-Sm ribonucleoprotein core
F: Like-Sm ribonucleoprotein core
G: Like-Sm ribonucleoprotein core


Theoretical massNumber of molelcules
Total (without water)71,2307
Polymers71,2307
Non-polymers00
Water90150
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12400 Å2
ΔGint-55 kcal/mol
Surface area23900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)197.214, 197.214, 38.880
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Detailsbiological unit is the same as asym.

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Components

#1: Protein
Like-Sm ribonucleoprotein core


Mass: 10175.745 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (strain 98/2) (archaea)
Strain: 98/2 / Gene: Ssol_1181 / Plasmid: pPROEX-Htb / Production host: Escherichia coli (E. coli) / Strain (production host): JW4130 deltahfq / References: UniProt: D0KRQ0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 0.1 M citric acid, 25% w/v polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.36
ReflectionResolution: 2.6→98.607 Å / Num. all: 17319 / Num. obs: 17319 / % possible obs: 100 % / Redundancy: 5.3 % / Rpim(I) all: 0.061 / Rrim(I) all: 0.141 / Rsym value: 0.127 / Net I/av σ(I): 4.815 / Net I/σ(I): 9.2 / Num. measured all: 91134
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.6-2.745.10.990.71277025190.490.992.1100
2.74-2.915.40.6431.11297123970.3040.6433.3100
2.91-3.115.30.4131.71187322490.1980.4134.8100
3.11-3.3650.23431054421010.1160.2347.2100
3.36-3.685.40.16441041319170.0770.16410.5100
3.68-4.115.30.1215.5929917390.0580.12113.1100
4.11-4.755.20.0817.9802615430.0390.08118.5100
4.75-5.815.50.0788.5709313000.0370.07817.2100
5.81-8.225.20.06910.1527310080.0330.06915.899.9
8.22-49.3045.30.05810.828725460.0280.05820.299.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.6 Å49.3 Å
Translation2.6 Å49.3 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
PHASER2.5.1phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1jri

1jri


Resolution: 2.6→49.303 Å / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 30.78 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1775 878 5.07 %
Rwork0.1409 16430 -
obs0.1442 17319 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 175.17 Å2 / Biso mean: 55.0035 Å2 / Biso min: 24.48 Å2
Refinement stepCycle: final / Resolution: 2.6→49.303 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4334 0 0 50 4384
Biso mean---48.08 -
Num. residues----552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064369
X-RAY DIFFRACTIONf_angle_d1.0915885
X-RAY DIFFRACTIONf_chiral_restr0.039716
X-RAY DIFFRACTIONf_plane_restr0.005744
X-RAY DIFFRACTIONf_dihedral_angle_d15.4641700
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6003-2.76310.32531640.25982699286394
2.7631-2.97620.24981450.21652773291895
2.9762-3.27530.20791480.17712735288395
3.2753-3.74830.16831380.15142724286295
3.7483-4.7190.15181420.11282749289195
4.719-28.46710.14331410.1122750289195
Refinement TLS params.Method: refined / Origin x: 134.3083 Å / Origin y: 148.0233 Å / Origin z: 95.0828 Å
111213212223313233
T0.3982 Å2-0.0295 Å20.0455 Å2-0.3251 Å20.1046 Å2--0.1619 Å2
L2.1943 °2-0.1531 °20.2541 °2-0.8179 °20.7661 °2--0.2909 °2
S-0.0622 Å °-0.0117 Å °-0.0237 Å °-0.02 Å °0.0077 Å °-0.034 Å °-0.0241 Å °-0.0814 Å °0.0577 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA7 - 84
2X-RAY DIFFRACTION1allB6 - 82
3X-RAY DIFFRACTION1allC6 - 82
4X-RAY DIFFRACTION1allD4 - 82
5X-RAY DIFFRACTION1allE6 - 82
6X-RAY DIFFRACTION1allF5 - 87
7X-RAY DIFFRACTION1allG5 - 85
8X-RAY DIFFRACTION1allS2 - 78

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